I found some posts that talked about possibly rebuilding the index in SonarQube and I tried, but it did not work. Now I am running out of options considering that in our test environment we do not see this behavior nor have I been able to spot any difference with the SonarQube configuration, scanner CLI or bamboo install and plans.

Does anyone have any idea what would be causing this and has anyone else seen this ?

This odd I am really confused we have a bunch of repos with branches against SonarQube community edition, They have been running for close to a year going to different branches just for scanning not comparison. And now i am wondering how are they actually working - is it a fluke?

My latest plan worked for a day in prod then it started throwing exception, but the DEV environment version is still working?.

Thanks again for the suggestion after a little bit of digging the issue appears to be related to the Sonar plugin that we are using within bamboo. Existing plans will keep on working but if I create a new one or make a modification through the GUI then after I save the “legacybranch” setting is set from “TRUE” to “” probably explaining why the plans begins to fail. I have contacted Mibex the vendor of the plugin and they are looking into it.